rs9513584

Variant names:

• chr13-99224027-G-A
• rs9513584
• NM_001144072.2:c.32-14400G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144072.2(UBAC2):​c.32-14400G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,022 control chromosomes in the GnomAD database, including 26,607 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.57 (26607 hom., cov: 32)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76
• Publications: 11 publications found

Genes affected

UBAC2 (HGNC:20486): (UBA domain containing 2) Involved in negative regulation of canonical Wnt signaling pathway and negative regulation of retrograde protein transport, ER to cytosol. Acts upstream of or within protein localization to endoplasmic reticulum. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBAC2	NM_001144072.2	c.32-14400G>A		intron_variant	Intron 1 of 8	ENST00000403766.8	NP_001137544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBAC2	ENST00000403766.8	c.32-14400G>A		intron_variant	Intron 1 of 8	2	NM_001144072.2	ENSP00000383911.3

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86642 AN: 151904 Hom.: 26597 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.572

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.570 AC: 86688 AN: 152022 Hom.: 26607 Cov.: 32 AF XY: 0.564 AC XY: 41890 AN XY: 74280

African (AFR) AF: 0.345 AC: 14321 AN: 41466

American (AMR) AF: 0.542 AC: 8275 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2212 AN: 3470

East Asian (EAS) AF: 0.501 AC: 2586 AN: 5164

South Asian (SAS) AF: 0.462 AC: 2228 AN: 4824

European-Finnish (FIN) AF: 0.629 AC: 6626 AN: 10540

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48245 AN: 67968

Other (OTH) AF: 0.570 AC: 1204 AN: 2112

Alfa AF: 0.628 Hom.: 4431

Bravo AF: 0.557

Asia WGS AF: 0.422 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.82
PhyloP100		-2.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9513584; hg19: chr13-99876281;